Recombinant Antibodies for the Generation of Antibody Arrays

Methods in Molecular Biology

Volumn 785, Issue , 2011, Pages 247-262

  Borrebaeck, Carl A K ^a   Wingren, Christer ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

Antibody arrays; Antibody design; Disease proteomics; Microarrays; Nanoarrays; Protein expression profiling; Recombinant antibodies; scFv

Indexed keywords

ANTIBODY; DIAGNOSTIC AGENT; RECOMBINANT PROTEIN;

ANTIBODY AFFINITY; ARTICLE; CHEMICAL STRUCTURE; GENE EXPRESSION PROFILING; HUMAN; METABOLISM; METHODOLOGY; PERSONALIZED MEDICINE; PROTEIN ENGINEERING; PROTEIN MICROARRAY; PROTEOMICS;

ANTIBODIES; ANTIBODY AFFINITY; GENE EXPRESSION PROFILING; HUMANS; INDIVIDUALIZED MEDICINE; MODELS, MOLECULAR; PROTEIN ARRAY ANALYSIS; PROTEIN ENGINEERING; PROTEOMICS; RECOMBINANT PROTEINS;

EID: 80054735822     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-286-1_17     Document Type: Chapter

References (86)

1. Borrebaeck, C. A., and Wingren, C. (2007) High-throughput proteomics using antibody microarrays: an update, Expert review of molecular diagnostics 7, 673–686.
2. Borrebaeck, C. A., and Wingren, C. (2009) Transferring proteomic discoveries into clinical practice, Expert review of proteomics 6, 11–13.
3. Haab, B. B. (2006) Applications of antibody array platforms, Current opinion in biotechnology.
4. Hartmann, M., Roeraade, J., Stoll, D., Templin, M. F., and Joos, T. O. (2009) Protein microarrays for diagnostic assays, Analytical and bioanalytical chemistry 393, 1407–1416.
5. Kingsmore, S. F. (2006) Multiplexed protein measurement: technologies and applications of protein and antibody arrays, Nature reviews 5, 310–320.
6. Wingren, C., and Borrebaeck, C. (2006) Antibody Microarrays-Current Status and Key Technological Advances, OMICS 10, 411–427.
7. Angenendt, P. (2005) Progress in protein and antibody microarray technology, Drug discovery today 10, 503–511.
8. MacBeath, G. (2002) Protein microarrays and proteomics, Nat Genet 32 Suppl, 526–532.
9. Svedhem, S., Pfeiffer, I., Larsson, C., Wingren, C., Borrebaeck, C., and Hook, F. (2003) Patterns of DNA-labeled and scFv-antibody-carrying lipid vesicles directed by material-specific immobilization of DNA and supported lipid bilayer formation on an Au/SiO2 template, Chembiochem 4, 339–343.
10. Wacker, R., and Niemeyer, C. M. (2004) DDI-microFIA--A readily configurable microarray-fluorescence immunoassay based on DNA-directed immobilization of proteins, Chembiochem 5, 453–459.
11. Wacker, R., Schroder, H., and Niemeyer, C. M. (2004) Performance of antibody microarrays fabricated by either DNA-directed immobilization, direct spotting, or streptavidin-biotin attachment: a comparative study, Anal Biochem 330, 281–287.
12. He, M., Stoevesandt, O., Palmer, E. A., Khan, F., Ericsson, O., and Taussig, M. J. (2008) Printing protein arrays from DNA arrays, Nature methods 5, 175–177.
13. He, M., Stoevesandt, O., and Taussig, M. J. (2008) In situ synthesis of protein arrays, Current opinion in biotechnology 19, 4–9.
14. He, M., and Taussig, M. J. (2001) Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method), Nucleic Acids Res 29, E73–73.
15. Ramachandran, N., Hainsworth, E., Bhullar, B., Eisenstein, S., Rosen, B., Lau, A. Y., Walter, J. C., and LaBaer, J. (2004) Self-assembling protein microarrays, Science 305, 86–90.
16. Ramachandran, N., Hainsworth, E., Demirkan, G., and LaBaer, J. (2006) On-chip protein synthesis for making microarrays, Methods in molecular biology Clifton, N.J 328, 1–14.
17. Ramachandran, N., Raphael, J. V., Hainsworth, E., Demirkan, G., Fuentes, M. G., Rolfs, A., Hu, Y., and LaBaer, J. (2008) Next-generation high-density self-assembling functional protein arrays, Nature methods 5, 535–538.
18. Joos, T. O., Stoll, D., and Templin, M. F. (2002) Miniaturised multiplexed immunoassays, Current opinion in chemical biology 6, 76–80.
19. Schwenk, J. M., Gry, M., Rimini, R., Uhlen, M., and Nilsson, P. (2008) Antibody suspension bead arrays within serum proteomics, Journal of proteome research 7, 3168–3179.
20. Templin, M. F., Stoll, D., Bachmann, J., and Joos, T. O. (2004) Protein microarrays and multiplexed sandwich immunoassays: what beats the beads?, Combinatorial chemistry & high throughput screening 7, 223–229.
21. Ingvarsson, J., Larsson, A., Sjoholm, A. G., Truedsson, L., Jansson, B., Borrebaeck, C. A., and Wingren, C. (2007) Design of recombinant antibody microarrays for serum protein profiling: targeting of complement proteins, Journal of proteome research 6, 3527–3536.
22. Kusnezow, W., Banzon, V., Schroder, C., Schaal, R., Hoheisel, J. D., Ruffer, S., Luft, P., Duschl, A., and Syagailo, Y. V. (2007) Antibody microarray-based profiling of complex specimens: systematic evaluation of labeling strategies, Proteomics 7, 1786–1799.
23. Wingren, C., Ingvarsson, J., Dexlin, L., Szul, D., and Borrebaeck, C. A. (2007) Design of recombinant antibody microarrays for complex proteome analysis: choice of sample labeling-tag and solid support, Proteomics 7, 3055–3065.
24. Haab, B. B. (2005) Multiplexed protein analysis using antibody microarrays and label-based detection, Methods Mol Med 114, 183–194.
25. Ellmark, P., Ingvarsson, J., Carlsson, A., Lundin, B. S., Wingren, C., and Borrebaeck, C. A. (2006) Identification of protein expression signatures associated with Helicobacter pylori infection and gastric adenocarcinoma using recombinant antibody microarrays, Mol Cell Proteomics 5, 1638–1646.
26. Haab, B. B. (2005) Antibody arrays in cancer research, Mol Cell Proteomics 4, 377–383.
27. Ingvarsson, J., Wingren, C., Carlsson, A., Ellmark, P., Wahren, B., Engstrom, G., Harmenberg, U., Krogh, M., Peterson, C., and Borrebaeck, C. A. (2008) Detection of pancreatic cancer using antibody microarray-based serum protein profiling, Proteomics 8, 2211–2219.
28. Orchekowski, R., Hamelinck, D., Li, L., Gliwa, E., vanBrocklin, M., Marrero, J. A., Vande Woude, G. F., Feng, Z., Brand, R., and Haab, B. B. (2005) Antibody microarray profiling reveals individual and combined serum proteins associated with pancreatic cancer, Cancer research 65, 11193–11202.
29. Sanchez-Carbayo, M., Socci, N. D., Lozano, J. J., Haab, B. B., and Cordon-Cardo, C. (2006) Profiling bladder cancer using targeted antibody arrays, Am J Pathol 168, 93–103.
30. Borrebaeck, C. A., and Wingren, C. (2009) Design of high-density antibody microarrays for disease proteomics: Key technological issues, Journal of proteomics.
31. Wingren, C., and Borrebaeck, C. A. (2004) High-throughput proteomics using antibody microarrays, Expert review of proteomics 1, 355–364.
32. Saerens, D., Ghassabeh, G. H., and Muyldermans, S. (2008) Antibody technology in proteomics, Brief Funct Genomic Proteomic 7, 275–282.
33. Renberg, B., Nordin, J., Merca, A., Uhlen, M., Feldwisch, J., Nygren, P. A., and Karlstrom, A. E. (2007) Affibody molecules in protein capture microarrays: evaluation of multidomain ligands and different detection formats, Journal of proteome research 6, 171–179.
34. Renberg, B., Shiroyama, I., Engfeldt, T., Nygren, P. K., and Karlstrom, A. E. (2005) Affibody protein capture microarrays: synthesis and evaluation of random and directed immobilization of affibody molecules, Anal Biochem 341, 334–343.
35. Lao, Y. H., Peck, K., and Chen, L. C. (2009) Enhancement of Aptamer Microarray Sensitivity through Spacer Optimization and Avidity Effect, Anal Chem.
36. Walter, J. G., Kokpinar, O., Friehs, K., Stahl, F., and Scheper, T. (2008) Systematic investigation of optimal aptamer immobilization for protein-microarray applications, Anal Chem 80, 7372–7378.
37. Cho, E. J., Collett, J. R., Szafranska, A. E., and Ellington, A. D. (2006) Optimization of aptamer microarray technology for multiple protein targets, Analytica chimica acta 564, 82–90.
38. Collett, J. R., Cho, E. J., Lee, J. F., Levy, M., Hood, A. J., Wan, C., and Ellington, A. D. (2005) Functional RNA microarrays for high-throughput screening of antiprotein aptamers, Anal Biochem 338, 113–123.
39. Campbell, C. J., O’Looney, N., Chong Kwan, M., Robb, J. S., Ross, A. J., Beattie, J. S., Petrik, J., and Ghazal, P. (2006) Cell interaction microarray for blood phenotyping, Anal Chem 78, 1930–1938.
40. Haab, B. B. (2003) Methods and applications of antibody microarrays in cancer research, Proteomics 3, 2116–2122.
41. Song, S., Li, B., Wang, L., Wu, H., Hu, J., Li, M., and Fan, C. (2007) A cancer protein microarray platform using antibody fragments and its clinical applications, Mol Biosyst 3, 151–158.
42. Wingren, C., Ingvarsson, J., Lindstedt, M., and Borrebaeck, C. A. (2003) Recombinant antibody microarrays–a viable option?, Nat Biotechnol 21, 223.
43. Pavlickova, P., Schneider, E. M., and Hug, H. (2004) Advances in recombinant antibody microarrays, Clin Chim Acta 343, 17–35.
44. Wingren, C., and Borrebaeck, C. A. (2008) Antibody microarray analysis of directly labelled complex proteomes, Current opinion in biotechnology 19, 55–61.
45. Kingsmore, S. F., and Patel, D. D. (2003) Multiplexed protein profiling on antibody-based microarrays by rolling circle amplification, Current opinion in biotechnology 14, 74–82.
46. Mitchell, P. (2002) A perspective on protein microarrays, Nature biotechnology 20, 225–229.
47. Haab, B. B., Dunham, M. J., and Brown, P. O. (2001) Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions, Genome Biol 2, RESEARCH0004.
48. Lefranc, M. P. (2004) IMGT-ONTOLOGY and IMGT databases, tools and Web resources for immunogenetics and immunoinformatics, Molecular immunology 40, 647–660.
49. Lefranc, M. P. (2008) IMGT, the International ImMunoGeneTics Information System for Immunoinformatics: methods for querying IMGT databases, tools, and web resources in the context of immunoinformatics, Mol Biotechnol 40, 101–111.
50. Barbas, C. F., 3rd, Kang, A. S., Lerner, R. A., and Benkovic, S. J. (1991) Assembly of combinatorial antibody libraries on phage surfaces: the gene III site, Proceedings of the National Academy of Sciences of the United States of America 88, 7978–7982.
51. Hanes, J., Schaffitzel, C., Knappik, A., and Pluckthun, A. (2000) Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display, Nat Biotechnol 18, 1287–1292.
52. Knappik, A., Ge, L., Honegger, A., Pack, P., Fischer, M., Wellnhofer, G., Hoess, A., Wolle, J., Pluckthun, A., and Virnekas, B. (2000) Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinu-cleotides, J Mol Biol 296, 57–86.
53. Lee, C. V., Liang, W. C., Dennis, M. S., Eigenbrot, C., Sidhu, S. S., and Fuh, G. (2004) High-affinity human antibodies from phage-displayed synthetic Fab libraries with a single framework scaffold, J Mol Biol 340, 1073–1093.
54. Marks, J. D., Hoogenboom, H. R., Bonnert, T. P., McCafferty, J., Griffiths, A. D., and Winter, G. (1991) By-passing immunization. Human antibodies from V-gene libraries displayed on phage, J Mol Biol 222, 581–597.
55. Soderlind, E., Strandberg, L., Jirholt, P., Kobayashi, N., Alexeiva, V., Aberg, A. M., Nilsson, A., Jansson, B., Ohlin, M., Wingren, C., Danielsson, L., Carlsson, R., and Borrebaeck, C. A. (2000) Recombining germline-derived CDR sequences for creating diverse single-framework antibody libraries, Nat Biotechnol 18, 852–856.
56. Angenendt, P., Wilde, J., Kijanka, G., Baars, S., Cahill, D. J., Kreutzberger, J., Lehrach, H., Konthur, Z., and Glokler, J. (2004) Seeing better through a MIST: evaluation of monoclonal recombinant antibody fragments on microarrays, Anal Chem 76, 2916–2921.
57. Cahill, D. J. (2001) Protein and antibody arrays and their medical applications, J Immunol Methods 250, 81–91.
58. Cahill, D. J., and Nordhoff, E. (2003) Protein arrays and their role in proteomics, Adv Biochem Eng Biotechnol 83, 177–187.
59. Wingren, C., and Borrebaeck, C. (2006) Recombinant Antibody Microarrays, Screening-Trends in Drug Discovery 2, 13–15.
60. Wingren, C., and Borrebaeck, C. A. (2009) Antibody-based microarrays, Methods in molecular biology Clifton, N.J 509, 57–84.
61. Seurynck-Servoss, S. L., Baird, C. L., Miller, K. D., Pefaur, N. B., Gonzalez, R. M., Apiyo, D. O., Engelmann, H. E., Srivastava, S., Kagan, J., Rodland, K. D., and Zangar, R. C. (2008) Immobilization strategies for single-chain antibody microarrays, Proteomics 8, 2199–2210.
62. Wingren, C., Steinhauer, C., Ingvarsson, J., Persson, E., Larsson, K., and Borrebaeck, C. A. (2005) Microarrays based on affinity-tagged single-chain Fv antibodies: sensitive detection of analyte in complex proteomes, Proteomics 5, 1281–1291.
63. Steinhauer, C., Wingren, C., Hager, A. C., and Borrebaeck, C. A. (2002) Single framework recombinant antibody fragments designed for protein chip applications, BioTechniques Suppl, 38–45.
64. Steinhauer, C., Wingren, C., Khan, F., He, M., Taussig, M. J., and Borrebaeck, C. A. (2006) Improved affinity coupling for antibody microarrays: Engineering of double-(His) (6)-tagged single framework recombinant antibody fragments, Proteomics 6, 4227–4234.
65. Wingren, C., and Borrebaeck, C. A. (2007) Progress in miniaturization of protein arrays--a step closer to high-density nanoarrays, Drug discovery today 12, 813–819.
66. Gulmann, C., Sheehan, K. M., Kay, E. W., Liotta, L. A., and Petricoin, E. F., 3rd. (2006) Array-based proteomics: mapping of protein circuitries for diagnostics, prognostics, and therapy guidance in cancer, The Journal of pathology 208, 595–606.
67. Utz, P. J. (2005) Protein arrays for studying blood cells and their secreted products, Immunological reviews 204, 264–282.
68. MacBeath, G., and Schreiber, S. L. (2000) Printing proteins as microarrays for high-throughput function determination, Science 289, 1760–1763.
69. Bailey, G. S. (1994) The raising of a polyclonal antiserum to a protein, Methods in molecular biology Clifton, N.J 32, 381–388.
70. Phelan, M. L., and Nock, S. (2003) Generation of bioreagents for protein chips, Proteomics 3, 2123–2134.
71. Agaton, C., Galli, J., Hoiden Guthenberg, I., Janzon, L., Hansson, M., Asplund, A., Brundell, E., Lindberg, S., Ruthberg, I., Wester, K., Wurtz, D., Hoog, C., Lundeberg, J., Stahl, S., Ponten, F., and Uhlen, M. (2003) Affinity proteomics for systematic protein profiling of chromosome 21 gene products in human tissues, Mol Cell Proteomics 2, 405–414.
72. Nilsson, P., Paavilainen, L., Larsson, K., Odling, J., Sundberg, M. r., Andersson, A.-C., Kampf, C., Persson, A., Szigyarto, C. A.-K., Ottosson, J., Bjorling, E., Hober, S., Wernérus, H., Wester, K., Pontén, F., and Uhlen, M. (2005) Towards a human proteome atlas: High-throughput generation of mono-specific antibodies for tissue profiling, Proteomics 5, 4327–4337.
73. Uhlen, M., Bjorling, E., Agaton, C., Szigyarto Cristina, A.-K., Amini, B., Andersen, E., Andersson, A.-C., Angelidou, P., Asplund, A., Asplund, C., Berglund, L., Bergstrom, K., Brumer, H., Cerjan, D., Ekstrom, M., Elobeid, A., Eriksson, C., Fagerberg, L., Falk, R., Fall, J., Forsberg, M., Bjorklund Marcus, G., Gumbel, K., Halimi, A., Hallin, I., Hamsten, C., Hansson, M., Hedhammar, M., Hercules, G., Kampf, C., Larsson, K., Lindskog, M., Lodewyckx, W., Lund, J., Lundeberg, J., Magnusson, K., Malm, E., Nilsson, P., Odling, J., Oksvold, P., Olsson, I., Oster, E., Ottosson, J., Paavilainen, L., Persson, A., Rimini, R., Rockberg, J., Runeson, M., Sivertsson, A., Skollermo, A., Steen, J., Stenvall, M., Sterky, F., Stromberg, S., Sundberg, M. r., Tegel, H., Tourle, S., Wahlund, E., Waldén, A., Wan, J., Wernérus, H., Westberg, J., Wester, K., Wrethagen, U., Xu Lan, L., Hober, S., and Pontén, F. (2005) A Human Protein Atlas for Normal and Cancer Tissues Based on Antibody Proteomics, Molecular & Cellular Proteomics 4, 1920–1932.
74. Borrebaeck, C. A., and Ohlin, M. (2002) Antibody evolution beyond Nature, Nature biotechnology 20, 1189–1190.
75. Hallborn, J., and Carlsson, R. (2002) Automated screening procedure for high-throughput generation of antibody fragments, BioTechniques Suppl, 30–37.
76. Wingren, C., James, P., and Borrebaeck, C. A. (2009) Strategy for surveying the proteome using affinity proteomics and mass spectrometry, Proteomics 9, 1511–1517.
77. Stoevesandt, O., and Taussig, M. J. (2007) Affinity reagent resources for human proteome detection: initiatives and perspectives, Proteomics 7, 2738–2750.
78. Hartmann, M., Schrenk, M., Dottinger, A., Nagel, S., Roeraade, J., Joos, T. O., and Templin, M. F. (2008) Expanding assay dynamics: a combined competitive and direct assay system for the quantification of proteins in multiplexed immunoassays, Clinical chemistry 54, 956–963.
79. Ewert, S., Huber, T., Honegger, A., and Pluckthun, A. (2003) Biophysical properties of human antibody variable domains, J Mol Biol 325, 531–553.
80. Worn, A., and Pluckthun, A. (2001) Stability engineering of antibody single-chain Fv fragments, J Mol Biol 305, 989–1010.
81. Ellmark, P., Ghatnekar-Nilsson, S., Meister, A., Heinzelmann, H., Montelius, L., Wingren, C., and Borrebaeck, C. A. (2009) Attovial-based antibody nanoarrays, Proteomics 9, 5406–5413.
82. Ghatnekar-Nilsson, S., Dexlin, L., Wingren, C., Montelius, L., and Borrebaeck, C. A. (2007) Design of atto-vial based recombinant antibody arrays combined with a planar wave-guide detection system, Proteomics 7, 540–547.
83. Dexlin, L., Ingvarsson, J., Frendeus, B., Borrebaeck, C.A.K., and Wingren, C. (2008) Design of recombinant antibody microarrays for cell surface membrane proteomics. J. Proteome Research 7, 319–327.
84. Lundberg, K., Lindstedt, M., Larsson, K., Dexlin, L., Wingren, C., Ohlin, M., Greiff, L., and Borrebaeck, C. A. (2008) Augmented Phl p 5-specific Th2 response after exposure of dendritic cells to allergen in complex with specific IgE compared to IgG1 and IgG4, Clinical immunology (Orlando, Fla 128, 358–365.
85. Carlsson, A., Wingren, C., Ingvarsson, J., Ellmark, P., Baldertorp, B., Ferno, M., Olsson, H., and Borrebaeck, C. A. (2008) Serum proteome profiling of metastatic breast cancer using recombinant antibody microarrays, Eur J Cancer 44, 472–480.
86. Carlsson, A., Persson, O., Widegren, B., Salford, L.G., Borrebaeck, C.A.K., and Wingren, C. (2010) Plasma protein profiling reveals biomarker patterns associated with prognosis and therapy selection in glioblastoma multiforme patients. Proteomics Clinical Applications 4, 591–602.